HEADER OXIDOREDUCTASE 02-JAN-02 1GS6 TITLE CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE TITLE 2 REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: NITRITE REDUCTASE, NIR; COMPND 5 EC: 1.7.99.3, 1.7.2.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 STRAIN: N.C.I.M.B. 11015; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PENIRM144A KEYWDS OXIDOREDUCTASE, MULTICOPPER, PERIPLASMIC EXPDTA X-RAY DIFFRACTION AUTHOR M.J.ELLIS,M.PRUDENCIO,F.E.DODD,R.W.STRANGE,G.SAWERS,R.R.EADY, AUTHOR 2 S.S.HASNAIN REVDAT 5 13-DEC-23 1GS6 1 REMARK LINK REVDAT 4 15-APR-15 1GS6 1 JRNL REVDAT 3 09-MAY-12 1GS6 1 COMPND REMARK VERSN DBREF REVDAT 3 2 1 FORMUL REVDAT 2 24-FEB-09 1GS6 1 VERSN REVDAT 1 14-FEB-02 1GS6 0 JRNL AUTH M.J.ELLIS,M.PRUDENCIO,F.E.DODD,R.W.STRANGE,G.SAWERS, JRNL AUTH 2 R.R.EADY,S.S.HASNAIN JRNL TITL BIOCHEMICAL AND CRYSTALLOGRAPHIC STUDIES OF THE MET144ALA, JRNL TITL 2 ASP92ASN AND HIS254PHE MUTANTS OF THE NITRITE REDUCTASE FROM JRNL TITL 3 ALCALIGENES XYLOSOXIDANS PROVIDE INSIGHT INTO THE ENZYME JRNL TITL 4 MECHANISM. JRNL REF J.MOL.BIOL. V. 316 51 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11829502 JRNL DOI 10.1006/JMBI.2001.5304 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 20082 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1505 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2572 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.172 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.786 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2511 ; 0.033 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2225 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 3433 ; 2.508 ; 1.936 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 5148 ; 1.525 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 382 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2866 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 493 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 369 ; 0.205 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1867 ; 0.213 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1 ; 0.220 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 184 ; 0.142 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 3 ; 0.197 ; 0.000 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.070 ; 0.000 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 11 ; 0.171 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 69 ; 0.185 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.206 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1638 ; 1.557 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2618 ; 2.604 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 873 ; 3.764 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 815 ; 5.417 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1GS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1290009143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 294.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI MONOCHROMATOR REMARK 200 OPTICS : RH COATED SI MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDN ENTRY 1NDT REMARK 200 REMARK 200 REMARK: COLLECTED USING OSCILLATION METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M MGCL2, 0.1M TRIS REMARK 280 -HCL PH8.5, TEMP GRADIENT 4-32 DEGREES C, PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.01300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.01300 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.01300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -157.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 -53.43000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 92.54347 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 53.43000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 92.54347 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED MUTATION: MET (144) ALA REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLN X 1 REMARK 475 ASP X 2 REMARK 475 PRO X 335 REMARK 475 ARG X 336 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP X 4 CB CG OD1 OD2 REMARK 480 LYS X 5 CB CG CD CE NZ REMARK 480 LYS X 10 CG CD CE NZ REMARK 480 GLU X 23 CD OE1 OE2 REMARK 480 LYS X 27 CG CD CE NZ REMARK 480 GLU X 40 CD OE1 OE2 REMARK 480 LYS X 42 CG CD CE NZ REMARK 480 ASP X 48 CB CG OD1 OD2 REMARK 480 LYS X 49 CG CD CE NZ REMARK 480 GLU X 133 CD OE1 OE2 REMARK 480 ASP X 154 CG OD1 OD2 REMARK 480 GLN X 160 CG CD OE1 NE2 REMARK 480 LYS X 162 CD CE NZ REMARK 480 ARG X 168 CG CD NE CZ NH1 NH2 REMARK 480 PRO X 183 O CB CG CD REMARK 480 ASP X 184 CB CG OD1 OD2 REMARK 480 LYS X 186 CB CG CD CE NZ REMARK 480 LYS X 217 CD CE NZ REMARK 480 LYS X 230 CG CD CE NZ REMARK 480 LYS X 315 CD CE NZ REMARK 480 GLU X 317 CD OE1 OE2 REMARK 480 LYS X 319 CD CE NZ REMARK 480 ASP X 322 CB CG OD1 OD2 REMARK 480 LYS X 326 CD CE NZ REMARK 480 LYS X 329 CB CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG X 168 OH TYR X 170 1.61 REMARK 500 OE1 GLN X 1 O HOH X 2001 1.68 REMARK 500 CZ ARG X 168 OH TYR X 170 1.79 REMARK 500 NE ARG X 168 OH TYR X 170 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP X 2 C ALA X 3 N -0.491 REMARK 500 LYS X 10 CB LYS X 10 CG -0.186 REMARK 500 GLU X 40 CG GLU X 40 CD 1.031 REMARK 500 ASP X 154 CB ASP X 154 CG 0.711 REMARK 500 PRO X 183 CA PRO X 183 CB 0.975 REMARK 500 PRO X 183 CD PRO X 183 N 0.746 REMARK 500 PRO X 183 C PRO X 183 O -0.420 REMARK 500 ASP X 184 CA ASP X 184 CB 0.172 REMARK 500 LYS X 217 CG LYS X 217 CD 0.317 REMARK 500 GLU X 317 CG GLU X 317 CD 0.381 REMARK 500 LYS X 319 CG LYS X 319 CD -0.230 REMARK 500 ILE X 334 C PRO X 335 N -0.551 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP X 2 O - C - N ANGL. DEV. = -20.3 DEGREES REMARK 500 ASP X 4 CA - CB - CG ANGL. DEV. = -17.0 DEGREES REMARK 500 ASP X 4 CB - CG - OD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 LYS X 5 N - CA - CB ANGL. DEV. = 14.8 DEGREES REMARK 500 GLU X 23 CB - CG - CD ANGL. DEV. = -20.8 DEGREES REMARK 500 GLU X 40 CB - CG - CD ANGL. DEV. = -35.1 DEGREES REMARK 500 GLU X 40 OE1 - CD - OE2 ANGL. DEV. = -10.8 DEGREES REMARK 500 GLU X 40 CG - CD - OE1 ANGL. DEV. = -32.8 DEGREES REMARK 500 GLU X 40 CG - CD - OE2 ANGL. DEV. = 23.5 DEGREES REMARK 500 LYS X 42 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 ASP X 92 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG X 122 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP X 154 CA - CB - CG ANGL. DEV. = -17.9 DEGREES REMARK 500 ASP X 154 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP X 167 CB - CG - OD2 ANGL. DEV. = 8.4 DEGREES REMARK 500 PRO X 183 C - N - CD ANGL. DEV. = -37.2 DEGREES REMARK 500 PRO X 183 CA - N - CD ANGL. DEV. = 32.7 DEGREES REMARK 500 PRO X 183 CB - CA - C ANGL. DEV. = 36.9 DEGREES REMARK 500 PRO X 183 N - CA - CB ANGL. DEV. = -39.5 DEGREES REMARK 500 PRO X 183 N - CD - CG ANGL. DEV. = -21.1 DEGREES REMARK 500 PRO X 183 CA - C - O ANGL. DEV. = -68.3 DEGREES REMARK 500 PRO X 183 O - C - N ANGL. DEV. = 22.5 DEGREES REMARK 500 ASP X 184 N - CA - CB ANGL. DEV. = -17.7 DEGREES REMARK 500 LYS X 217 CB - CG - CD ANGL. DEV. = -22.1 DEGREES REMARK 500 ARG X 247 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 LYS X 315 CB - CG - CD ANGL. DEV. = -16.1 DEGREES REMARK 500 LYS X 319 CB - CG - CD ANGL. DEV. = 20.0 DEGREES REMARK 500 ILE X 334 CA - C - N ANGL. DEV. = 49.4 DEGREES REMARK 500 ILE X 334 O - C - N ANGL. DEV. = -50.8 DEGREES REMARK 500 PRO X 335 C - N - CA ANGL. DEV. = 34.3 DEGREES REMARK 500 PRO X 335 C - N - CD ANGL. DEV. = -36.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN X 24 -85.22 -73.68 REMARK 500 PRO X 30 132.80 -37.45 REMARK 500 ALA X 131 64.46 -151.05 REMARK 500 ILE X 334 95.90 -50.66 REMARK 500 PRO X 335 124.65 -23.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU X 23 0.07 SIDE CHAIN REMARK 500 GLU X 40 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP X 2 -26.92 REMARK 500 PRO X 183 22.37 REMARK 500 ILE X 334 26.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU X1337 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 89 ND1 REMARK 620 2 CYS X 130 SG 120.0 REMARK 620 3 HIS X 139 ND1 106.2 122.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU X1338 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 94 NE2 REMARK 620 2 HIS X 129 NE2 112.7 REMARK 620 3 HIS X 300 NE2 103.5 104.1 REMARK 620 4 HOH X2045 O 99.2 111.8 125.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X1339 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU X 260 O REMARK 620 2 ARG X 278 N 128.3 REMARK 620 3 SER X 281 OG 126.8 75.6 REMARK 620 N 1 2 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU X 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU X 1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1339 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1GS8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D92N MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1HAU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 1HAW RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9 ANGSTROMS RESOLUTION DBREF 1GS6 X 1 336 UNP O68601 O68601_ALCXX 25 360 SEQADV 1GS6 ALA X 144 UNP O68601 MET 168 ENGINEERED MUTATION SEQRES 1 X 336 GLN ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 X 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 X 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 X 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 X 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 X 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 X 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 X 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 X 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 X 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS SEQRES 11 X 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 X 336 ALA SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 X 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 X 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 X 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 X 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 X 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 X 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 X 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 X 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 X 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 X 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 X 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 X 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 X 336 HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 X 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG HET CU X1337 1 HET CU X1338 1 HET MG X1339 1 HETNAM CU COPPER (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 CU 2(CU 2+) FORMUL 4 MG MG 2+ FORMUL 5 HOH *153(H2 O) HELIX 1 1 GLY X 98 THR X 106 5 9 HELIX 2 2 MET X 135 SER X 142 1 8 HELIX 3 3 THR X 192 ARG X 205 1 14 HELIX 4 4 THR X 222 ALA X 226 5 5 HELIX 5 5 ASN X 301 GLU X 307 1 7 SHEET 1 XA 4 HIS X 8 LYS X 10 0 SHEET 2 XA 4 VAL X 32 VAL X 45 1 O VAL X 32 N THR X 9 SHEET 3 XA 4 TYR X 74 ASN X 81 1 O TYR X 74 N VAL X 33 SHEET 4 XA 4 GLU X 112 LYS X 119 -1 O GLU X 112 N ASN X 81 SHEET 1 XB 3 HIS X 8 LYS X 10 0 SHEET 2 XB 3 VAL X 32 VAL X 45 1 O VAL X 32 N THR X 9 SHEET 3 XB 3 THR X 52 PHE X 58 -1 O LEU X 53 N MET X 44 SHEET 1 XC 4 LEU X 67 HIS X 70 0 SHEET 2 XC 4 SER X 145 LEU X 151 1 O THR X 147 N LEU X 67 SHEET 3 XC 4 GLY X 124 HIS X 129 -1 O GLY X 124 N VAL X 150 SHEET 4 XC 4 ASP X 92 PHE X 93 -1 O ASP X 92 N HIS X 129 SHEET 1 XD 6 HIS X 211 PHE X 214 0 SHEET 2 XD 6 ARG X 168 LEU X 177 -1 O PHE X 175 N VAL X 213 SHEET 3 XD 6 THR X 234 GLN X 241 1 O LEU X 236 N TYR X 170 SHEET 4 XD 6 SER X 281 THR X 288 -1 O SER X 281 N GLN X 241 SHEET 5 XD 6 GLY X 255 TRP X 259 -1 N ASP X 256 O LEU X 286 SHEET 6 XD 6 GLN X 269 LEU X 272 -1 O GLN X 269 N VAL X 258 SHEET 1 XE 4 LEU X 227 LYS X 230 0 SHEET 2 XE 4 ALA X 311 GLU X 317 1 O HIS X 313 N LEU X 227 SHEET 3 XE 4 GLY X 293 ASN X 299 -1 O GLY X 293 N VAL X 316 SHEET 4 XE 4 PRO X 248 ILE X 251 -1 O HIS X 249 N LEU X 298 LINK ND1 HIS X 89 CU CU X1337 1555 1555 2.12 LINK NE2 HIS X 94 CU CU X1338 1555 1555 2.01 LINK NE2 HIS X 129 CU CU X1338 1555 1555 2.13 LINK SG CYS X 130 CU CU X1337 1555 1555 2.22 LINK ND1 HIS X 139 CU CU X1337 1555 1555 1.92 LINK O GLU X 260 MG MG X1339 1555 1555 2.87 LINK N ARG X 278 MG MG X1339 1555 1555 3.02 LINK OG SER X 281 MG MG X1339 1555 1555 2.76 LINK NE2 HIS X 300 CU CU X1338 2665 1555 2.15 LINK CU CU X1338 O HOH X2045 1555 1555 1.95 CISPEP 1 PRO X 16 PRO X 17 0 4.46 CISPEP 2 MET X 62 PRO X 63 0 -4.35 SITE 1 AC1 3 HIS X 89 CYS X 130 HIS X 139 SITE 1 AC2 6 ASP X 92 HIS X 94 HIS X 129 HIS X 300 SITE 2 AC2 6 HOH X2045 HOH X2066 SITE 1 AC3 5 GLU X 260 THR X 261 ILE X 277 ARG X 278 SITE 2 AC3 5 SER X 281 CRYST1 106.860 106.860 64.026 90.00 90.00 120.00 P 63 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009358 0.005403 0.000000 0.00000 SCALE2 0.000000 0.010806 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015619 0.00000